data_PYO
#
_chem_comp.id PYO
_chem_comp.name "1-(BETA-D-RIBOFURANOSYL)-PYRIMIDIN-2-ONE-5'-PHOSPHATE"
_chem_comp.type "RNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C9 H13 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id U
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-09-13
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 308.182
_chem_comp.one_letter_code U
_chem_comp.three_letter_code PYO
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
PYO OP3 O3P O 0 1 N Y N N N N -16.115 106.143 5.841 -1.825 1.007 -4.603 OP3 PYO 1
PYO P P P 0 1 N N N N N N -15.321 107.173 6.777 -0.773 0.044 -3.855 P PYO 2
PYO OP1 O1P O 0 1 N N N N N N -15.917 107.091 8.137 0.502 -0.196 -4.805 OP1 PYO 3
PYO OP2 O2P O 0 1 N N N N N N -15.244 108.489 6.093 -1.419 -1.253 -3.557 OP2 PYO 4
PYO "O5'" O5* O 0 1 N N N N N N -13.845 106.592 6.871 -0.297 0.735 -2.481 "O5'" PYO 5
PYO "C5'" C5* C 0 1 N N N N N N -12.839 107.388 7.463 0.629 -0.163 -1.867 "C5'" PYO 6
PYO "C4'" C4* C 0 1 N N R N N N -11.479 106.765 7.312 1.123 0.436 -0.549 "C4'" PYO 7
PYO "O4'" O4* O 0 1 N N N N N N -11.264 106.277 5.958 0.018 0.625 0.364 "O4'" PYO 8
PYO "C3'" C3* C 0 1 N N S N N N -10.391 107.794 7.565 2.068 -0.547 0.176 "C3'" PYO 9
PYO "C1'" C1* C 0 1 N N R N N N -10.199 106.995 5.356 0.615 0.707 1.676 "C1'" PYO 10
PYO "O3'" O3* O 0 1 N N N N N N -9.271 107.152 8.144 3.433 -0.205 -0.070 "O3'" PYO 11
PYO "C2'" C2* C 0 1 N N R N N N -10.087 108.295 6.157 1.726 -0.366 1.672 "C2'" PYO 12
PYO "O2'" O2* O 0 1 N N N N N N -8.814 108.902 6.048 2.870 0.089 2.395 "O2'" PYO 13
PYO N1 N1 N 0 1 N N N N N N -10.486 107.151 3.915 -0.377 0.409 2.711 N1 PYO 14
PYO C6 C6 C 0 1 N N N N N N -11.658 106.769 3.415 -0.606 1.302 3.708 C6 PYO 15
PYO C2 C2 C 0 1 N N N N N N -9.482 107.700 3.104 -1.066 -0.746 2.668 C2 PYO 16
PYO C5 C5 C 0 1 N N N N N N -11.885 106.900 2.097 -1.531 1.010 4.661 C5 PYO 17
PYO O2 O2 O 0 1 N N N N N N -8.371 108.077 3.581 -0.852 -1.540 1.767 O2 PYO 18
PYO N3 N3 N 0 1 N N N N N N -9.730 107.823 1.767 -1.972 -1.041 3.603 N3 PYO 19
PYO C4 C4 C 0 1 N N N N N N -10.900 107.427 1.299 -2.223 -0.201 4.588 C4 PYO 20
PYO HOP3 3HOP H 0 0 N N N N N N -15.734 106.195 4.972 -2.084 0.558 -5.419 HOP3 PYO 21
PYO HOP1 1HOP H 0 0 N N N N N N -15.446 107.701 8.691 0.893 0.671 -4.975 HOP1 PYO 22
PYO "H5''" 2H5* H 0 0 N N N N N N -12.856 108.429 7.064 0.136 -1.115 -1.671 "H5''" PYO 23
PYO "H5'" 1H5* H 0 1 N N N N N N -13.069 107.607 8.531 1.476 -0.322 -2.534 "H5'" PYO 24
PYO "H4'" H4* H 0 1 N N N N N N -11.434 105.927 8.046 1.631 1.383 -0.731 "H4'" PYO 25
PYO "H3'" H3* H 0 1 N N N N N N -10.672 108.617 8.262 1.869 -1.571 -0.140 "H3'" PYO 26
PYO "H1'" H1* H 0 1 N N N N N N -9.207 106.485 5.387 1.044 1.696 1.836 "H1'" PYO 27
PYO HO3 3HO H 0 1 N Y N N N N -8.590 107.795 8.302 3.973 -0.831 0.430 HO3 PYO 28
PYO "H2'" H2* H 0 1 N N N N N N -10.767 109.106 5.806 1.356 -1.300 2.094 "H2'" PYO 29
PYO HO2 2HO H 0 1 N N N N N N -8.624 109.214 5.170 3.548 -0.593 2.306 HO2 PYO 30
PYO HC6 HC6 H 0 1 N N N N N N -12.429 106.350 4.082 -0.059 2.233 3.745 HC6 PYO 31
PYO HC5 HC5 H 0 1 N N N N N N -12.855 106.582 1.680 -1.729 1.706 5.464 HC5 PYO 32
PYO HC4 HC4 H 0 1 N N N N N N -11.058 107.539 0.213 -2.962 -0.450 5.336 HC4 PYO 33
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
PYO OP3 P SING N N 1
PYO OP3 HOP3 SING N N 2
PYO P OP1 SING N N 3
PYO P OP2 DOUB N N 4
PYO P "O5'" SING N N 5
PYO OP1 HOP1 SING N N 6
PYO "O5'" "C5'" SING N N 7
PYO "C5'" "C4'" SING N N 8
PYO "C5'" "H5''" SING N N 9
PYO "C5'" "H5'" SING N N 10
PYO "C4'" "O4'" SING N N 11
PYO "C4'" "C3'" SING N N 12
PYO "C4'" "H4'" SING N N 13
PYO "O4'" "C1'" SING N N 14
PYO "C3'" "O3'" SING N N 15
PYO "C3'" "C2'" SING N N 16
PYO "C3'" "H3'" SING N N 17
PYO "C1'" "C2'" SING N N 18
PYO "C1'" N1 SING N N 19
PYO "C1'" "H1'" SING N N 20
PYO "O3'" HO3 SING N N 21
PYO "C2'" "O2'" SING N N 22
PYO "C2'" "H2'" SING N N 23
PYO "O2'" HO2 SING N N 24
PYO N1 C6 SING N N 25
PYO N1 C2 SING N N 26
PYO C6 C5 DOUB N N 27
PYO C6 HC6 SING N N 28
PYO C2 O2 DOUB N N 29
PYO C2 N3 SING N N 30
PYO C5 C4 SING N N 31
PYO C5 HC5 SING N N 32
PYO N3 C4 DOUB N N 33
PYO C4 HC4 SING N N 34
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
PYO SMILES ACDLabs 10.04 O=C1N=CC=CN1C2OC(C(O)C2O)COP(=O)(O)O
PYO SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC=NC2=O
PYO SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC=NC2=O
PYO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
PYO SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1)C2C(C(C(O2)COP(=O)(O)O)O)O
PYO InChI InChI 1.03 InChI=1S/C9H13N2O8P/c12-6-5(4-18-20(15,16)17)19-8(7(6)13)11-3-1-2-10-9(11)14/h1-3,5-8,12-13H,4H2,(H2,15,16,17)/t5-,6-,7-,8-/m1/s1
PYO InChIKey InChI 1.03 LBWXMAFPEFFHIJ-WCTZXXKLSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
PYO "SYSTEMATIC NAME" ACDLabs 10.04 1-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidin-2(1H)-one
PYO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxopyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PYO 'Create component' 2000-09-13 EBI
PYO 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
PYO OP3 O 11.218 -5.146 1
PYO P P 10.336 -3.933 2
PYO OP1 O 11.550 -3.051 3
PYO OP2 O 9.123 -4.814 4
PYO "O5'" O 9.455 -2.719 5
PYO "C5'" C 7.963 -2.876 6
PYO "C4'" C 7.081 -1.662 7
PYO "O4'" O 7.545 -0.236 8
PYO "C3'" C 5.581 -1.662 9
PYO "C1'" C 6.331 0.646 10
PYO "O3'" O 4.699 -2.876 11
PYO "C2'" C 5.118 -0.236 12
PYO "O2'" O 3.691 0.228 13
PYO N1 N 6.331 2.146 14
PYO C6 C 5.032 2.896 15
PYO C2 C 7.630 2.896 16
PYO C5 C 5.032 4.396 17
PYO O2 O 8.929 2.146 18
PYO N3 N 7.630 4.396 19
PYO C4 C 6.331 5.146 20
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
PYO OP3 P SINGLE NONE 1
PYO P OP1 SINGLE NONE 2
PYO P OP2 DOUBLE NONE 3
PYO P "O5'" SINGLE NONE 4
PYO "O5'" "C5'" SINGLE NONE 5
PYO "C4'" "C5'" SINGLE BEGINDASH 6
PYO "C4'" "O4'" SINGLE NONE 7
PYO "C4'" "C3'" SINGLE NONE 8
PYO "O4'" "C1'" SINGLE NONE 9
PYO "C3'" "O3'" SINGLE BEGINWEDGE 10
PYO "C3'" "C2'" SINGLE NONE 11
PYO "C1'" "C2'" SINGLE NONE 12
PYO "C1'" N1 SINGLE BEGINDASH 13
PYO "C2'" "O2'" SINGLE BEGINWEDGE 14
PYO N1 C6 SINGLE NONE 15
PYO N1 C2 SINGLE NONE 16
PYO C6 C5 DOUBLE NONE 17
PYO C2 O2 DOUBLE NONE 18
PYO C2 N3 SINGLE NONE 19
PYO C5 C4 SINGLE NONE 20
PYO N3 C4 DOUBLE NONE 21
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
PYO MurckoScaffold S1 scaffold 'O=c1ncccn1[C@H]1CCCO1' InChI=1S/C8H10N2O2/c11-8-9-4-2-5-10(8)7-3-1-6-12-7/h2,4-5,7H,1,3,6H2/t7-/m1/s1 AKXKPKRAUWTVBW-SSDOTTSWSA-N
PYO phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
PYO pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
PYO ribose F3 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
PYO "C4'" S1 1
PYO "O4'" S1 1
PYO "C3'" S1 1
PYO "C1'" S1 1
PYO "C2'" S1 1
PYO N1 S1 1
PYO C6 S1 1
PYO C2 S1 1
PYO C5 S1 1
PYO O2 S1 1
PYO N3 S1 1
PYO C4 S1 1
PYO OP3 F1 1
PYO P F1 1
PYO OP2 F1 1
PYO OP1 F1 1
PYO "O5'" F1 1
PYO C5 F2 1
PYO C6 F2 1
PYO N1 F2 1
PYO C2 F2 1
PYO N3 F2 1
PYO C4 F2 1
PYO "C2'" F3 1
PYO "C3'" F3 1
PYO "C4'" F3 1
PYO "O4'" F3 1
PYO "C1'" F3 1
PYO "C5'" F3 1
PYO "O5'" F3 1
PYO "O3'" F3 1
PYO "O2'" F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PYO
_pdbe_chem_comp_rdkit_properties.exactmw 308.041
_pdbe_chem_comp_rdkit_properties.amw 308.183
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 130.626
_pdbe_chem_comp_rdkit_properties.tpsa 151.340
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.128
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.525
_pdbe_chem_comp_rdkit_properties.chi0v 10.002
_pdbe_chem_comp_rdkit_properties.chi1v 6.034
_pdbe_chem_comp_rdkit_properties.chi2v 2.140
_pdbe_chem_comp_rdkit_properties.chi3v 2.140
_pdbe_chem_comp_rdkit_properties.chi4v 1.288
_pdbe_chem_comp_rdkit_properties.chi0n 22.108
_pdbe_chem_comp_rdkit_properties.chi1n 10.706
_pdbe_chem_comp_rdkit_properties.chi2n 1.825
_pdbe_chem_comp_rdkit_properties.chi3n 1.825
_pdbe_chem_comp_rdkit_properties.chi4n 1.093
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.130
_pdbe_chem_comp_rdkit_properties.kappa1 5.577
_pdbe_chem_comp_rdkit_properties.kappa2 5.700
_pdbe_chem_comp_rdkit_properties.kappa3 3.302
_pdbe_chem_comp_rdkit_properties.Phi 1.590
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
PYO UniChem ZINC ZINC000016052085
PYO UniChem PubChem 16040244
PYO UniChem Nikkaji J395.119G
PYO UniChem BRENDA 98833
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
PYO OP3 4.709 1.341 -0.523 ETKDGv3 1
PYO P 3.242 2.069 -0.092 ETKDGv3 2
PYO OP1 2.880 3.283 -1.213 ETKDGv3 3
PYO OP2 3.366 2.686 1.284 ETKDGv3 4
PYO "O5'" 1.987 0.915 -0.104 ETKDGv3 5
PYO "C5'" 2.340 -0.138 0.763 ETKDGv3 6
PYO "C4'" 1.213 -1.175 0.807 ETKDGv3 7
PYO "O4'" 0.033 -0.574 1.301 ETKDGv3 8
PYO "C3'" 0.932 -1.788 -0.580 ETKDGv3 9
PYO "C1'" -1.028 -1.054 0.511 ETKDGv3 10
PYO "O3'" 1.003 -3.191 -0.515 ETKDGv3 11
PYO "C2'" -0.481 -1.337 -0.875 ETKDGv3 12
PYO "O2'" -1.241 -2.325 -1.522 ETKDGv3 13
PYO N1 -2.130 -0.079 0.461 ETKDGv3 14
PYO C6 -3.490 -0.551 0.473 ETKDGv3 15
PYO C2 -1.910 1.337 0.296 ETKDGv3 16
PYO C5 -4.509 0.308 0.375 ETKDGv3 17
PYO O2 -0.746 1.813 0.228 ETKDGv3 18
PYO N3 -3.036 2.215 0.203 ETKDGv3 19
PYO C4 -4.251 1.754 0.241 ETKDGv3 20
PYO HOP3 5.360 2.087 -0.557 ETKDGv3 21
PYO HOP1 1.971 3.591 -0.966 ETKDGv3 22
PYO "H5''" 3.269 -0.645 0.414 ETKDGv3 23
PYO "H5'" 2.498 0.238 1.800 ETKDGv3 24
PYO "H4'" 1.518 -1.973 1.520 ETKDGv3 25
PYO "H3'" 1.620 -1.410 -1.373 ETKDGv3 26
PYO "H1'" -1.388 -2.004 0.972 ETKDGv3 27
PYO HO3 1.968 -3.423 -0.505 ETKDGv3 28
PYO "H2'" -0.460 -0.399 -1.479 ETKDGv3 29
PYO HO2 -0.927 -2.346 -2.463 ETKDGv3 30
PYO HC6 -3.700 -1.610 0.562 ETKDGv3 31
PYO HC5 -5.528 -0.055 0.389 ETKDGv3 32
PYO HC4 -5.084 2.440 0.168 ETKDGv3 33
#